James A. Fellows Yates
|
7353fb257d
|
Merge pull request #380 from jfy133/taxprofiler
Add MAG @ EVA profile
|
2022-06-03 12:54:47 +02:00 |
|
James Fellows Yates
|
5a67eba04c
|
Add MAG @ EVA profile
|
2022-06-03 12:41:08 +02:00 |
|
Emil Bertilsson
|
80e2a50a2f
|
Merge pull request #378 from raysloks/feat/hasta_java_memory_fix
Feat/hasta java memory fix
|
2022-05-30 14:40:52 +02:00 |
|
Emil
|
8453f6b41a
|
Moves qualimap arg to pipeline-specific config
|
2022-05-30 12:58:12 +02:00 |
|
Emil
|
29fa08c434
|
Adds _JAVA_OPTIONS to singularity whitelist
|
2022-05-30 11:07:24 +02:00 |
|
Emil
|
19497a4183
|
Makes qualimap fix work for most memory amounts
|
2022-05-30 11:06:48 +02:00 |
|
Nicolas Vannieuwkerke
|
c2b26a734d
|
automated the internal cache dir location for singularity
|
2022-05-20 09:48:19 +02:00 |
|
Nicolas Vannieuwkerke
|
cc86e6b270
|
Added the VSC UGent profile
|
2022-05-20 09:12:18 +02:00 |
|
Sarah Guinchard
|
be9711731a
|
Merge pull request #375 from nf-core/ifb_core-config-update
Ifb core config update
|
2022-05-13 14:45:44 +02:00 |
|
Sarah Guinchard
|
3538f8511a
|
removed comment
|
2022-05-12 11:02:42 +02:00 |
|
sofstam
|
54b3cda34d
|
Add review suggestion
|
2022-05-12 11:00:26 +02:00 |
|
Sarah Guinchard
|
6bb7c1a422
|
Update config file with queue & correct ressources
|
2022-05-12 10:55:00 +02:00 |
|
sofstam
|
c59149d64c
|
Update docs for hasta config
|
2022-05-12 10:47:03 +02:00 |
|
James Fellows Yates
|
e1f780d976
|
Add taxprofiler for eVA
|
2022-05-12 07:54:17 +01:00 |
|
sofstam
|
5bc6ed90bd
|
Add hasta config for taxprofiler
|
2022-05-11 11:13:31 +02:00 |
|
Thiseas C. Lamnidis
|
d09f5fc116
|
Update eva.config
eigenstrat_snp_coverage also loads pandas
|
2022-05-06 15:12:04 +02:00 |
|
James A. Fellows Yates
|
8fbfcfe256
|
Merge pull request #371 from jfy133/master
Rename custom log file for EVA
|
2022-05-06 14:02:03 +02:00 |
|
James A. Fellows Yates
|
95d18270e8
|
Update eva.config
|
2022-05-06 13:57:11 +02:00 |
|
Emil
|
e938f3606f
|
Removes the new SGE clusterOptions for now
|
2022-05-05 14:09:45 +02:00 |
|
Harshil Patel
|
20c826fd50
|
Update retry strategy for preemptible instances on GCP
|
2022-05-05 11:10:05 +01:00 |
|
Emil
|
8b9744723c
|
Fixes hasta java memory issues
|
2022-05-04 14:13:24 +02:00 |
|
Thiseas C. Lamnidis
|
209601f782
|
missing bracket
|
2022-05-04 13:08:13 +02:00 |
|
Thiseas C. Lamnidis
|
a42c4344ad
|
Exclude bionode 06 for software versions
|
2022-05-03 18:30:42 +02:00 |
|
Thiseas C. Lamnidis
|
79e227aa4e
|
Update eva.config
|
2022-05-03 16:42:21 +02:00 |
|
Thiseas C. Lamnidis
|
085726d081
|
Update eva.config
|
2022-05-03 16:36:05 +02:00 |
|
Thiseas C. Lamnidis
|
4592969613
|
memory for get_software_versions in MB.
|
2022-05-03 16:30:04 +02:00 |
|
Thiseas C. Lamnidis
|
79ad571319
|
Update eva.config
|
2022-05-03 16:25:48 +02:00 |
|
Thiseas C. Lamnidis
|
04226692fe
|
Update eva.config
|
2022-05-03 16:21:35 +02:00 |
|
Thiseas C. Lamnidis
|
57095fe79f
|
Update eva.config
Set max heap size for java jobs in `get_software_versions`.
Limited OpenBLAS threading for python jobs that use numpy/pandas.
|
2022-05-03 16:12:20 +02:00 |
|
James A. Fellows Yates
|
b5d9b79377
|
Merge branch 'nf-core:master' into master
|
2022-05-02 13:59:18 +02:00 |
|
James A. Fellows Yates
|
bf658abc77
|
Update eva.config
|
2022-05-02 13:59:13 +02:00 |
|
Alex Rajewski
|
69d1a14894
|
basic Cedars-Sinai HPC config file
|
2022-04-22 10:17:13 -07:00 |
|
James A. Fellows Yates
|
c1425c6c01
|
Merge pull request #364 from jfy133/eva-update
Update eager @ eva.config to allow retry on post-processing FASTQ
|
2022-04-22 11:47:10 +02:00 |
|
James A. Fellows Yates
|
a086878c0b
|
Update eva.config
|
2022-04-22 10:47:04 +02:00 |
|
Praveen Raj S
|
edaad1cd18
|
Update: sentieon version
Sentieon version has been updated to 202112.02.
|
2022-04-07 12:36:01 +02:00 |
|
James A. Fellows Yates
|
44238471cf
|
Update eva.config
|
2022-03-31 13:12:50 +02:00 |
|
James Fellows Yates
|
2277b541a3
|
Re-add bash bin specification
|
2022-03-31 11:06:53 +02:00 |
|
James A. Fellows Yates
|
8ad4ddac6a
|
Merge branch 'master' into fix-eva
|
2022-03-29 12:50:54 +02:00 |
|
James Fellows Yates
|
3d2a612b39
|
Remove setting of bash in clusterOotions
|
2022-03-29 12:48:37 +02:00 |
|
James A. Fellows Yates
|
576351219a
|
Update eva.config
|
2022-03-29 12:47:46 +02:00 |
|
James A. Fellows Yates
|
9e502025b9
|
Merge pull request #358 from aidaanva/master
Update eva.config bigmem.q
|
2022-03-28 09:11:18 +02:00 |
|
Mahesh Binzer-Panchal
|
3a7f7f431e
|
Execute sinfo with bash shell
|
2022-03-25 13:58:37 +00:00 |
|
Aida Andrades Valtueña
|
b9da0b4f00
|
Update eva.config
Update eva.config to send big memory jobs (>700G) to the bigmem queue
|
2022-03-25 09:36:29 +01:00 |
|
b97pla
|
9a6cdfc21e
|
removed process-specific requirements for sarek, request miarka high-mem node
|
2022-03-24 14:25:43 +01:00 |
|
b97pla
|
5466d927f1
|
added requirements for uppmax cluster miarka
|
2022-03-23 15:29:40 +01:00 |
|
James A. Fellows Yates
|
962d86d604
|
Merge pull request #346 from sagc-bioinformatics/sahmri
Added SAHMRI profile
|
2022-03-18 13:01:36 +01:00 |
|
Nathan S. Watson-Haigh
|
30f710ada4
|
Add debug profile
|
2022-03-17 13:38:43 +10:30 |
|
Praveen Raj S
|
1d4f254e43
|
Update munin.config
|
2022-03-16 14:37:28 +01:00 |
|
Praveen Raj S
|
9747d5fe15
|
Added PileupSummariesForMutect2 in CPU limit list
Add PileupSummariesForMutect2 to the list to run with less threads.
Changed the MaxForks to 12
Tested on an internal sample and it worked!
|
2022-03-16 14:36:25 +01:00 |
|
Alexander Peltzer
|
d510cb254e
|
Merge pull request #165 from ewels/fix-show-profiles
Set params.custom_config_base in nextflow.config
|
2022-03-15 17:13:24 +01:00 |
|